Contacts of the helix formed by residues 176 - 195 (chain A) in PDB entry 3LX9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A CYS* 3.3 11.4 - - - -
175A ASP* 1.3 85.2 + - - +
177A LEU* 1.3 61.4 + - - +
178A GLU* 3.6 8.5 + - - +
179A ASN* 3.2 28.4 + - - +
180A LEU* 3.0 22.1 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A SER* 1.3 72.6 - - - +
178A GLU* 1.3 59.7 + - - +
180A LEU* 3.3 24.8 - - + +
181A ALA* 2.9 29.5 + - - +
204A TRP* 5.5 0.2 + - - -
207A TYR* 3.6 24.2 - - + +
208A MET* 4.3 11.4 - - + -
211A PHE* 4.3 19.5 - - + -
212A GLN* 3.2 53.6 - - + +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 3.3 8.7 + - - +
177A LEU* 1.3 78.9 - - - +
179A ASN* 1.3 63.5 + - - +
181A ALA* 3.3 5.0 + - - +
182A ASP* 3.0 49.2 + - - +
212A GLN* 5.5 0.4 - - - +
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Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 4.5 1.9 - - - +
149A PHE* 4.4 11.1 - - + -
152A TYR* 4.7 2.1 + - - -
174A CYS* 3.8 9.9 - - - -
175A ASP* 3.0 25.7 - - - +
176A SER* 3.2 17.0 + - - +
178A GLU* 1.3 80.6 - - - +
180A LEU* 1.3 60.7 + - - +
182A ASP* 3.9 10.7 + - - +
183A GLY* 2.9 26.5 + - - -
639A NAG 3.8 21.5 + - + +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.9 8.5 - - + +
171A GLY* 3.7 36.1 - - - +
174A CYS* 3.4 13.4 - - + -
176A SER 3.0 16.0 + - - +
177A LEU* 3.3 30.3 - - + +
178A GLU 3.2 0.2 - - - -
179A ASN* 1.3 76.9 - - - +
181A ALA* 1.3 61.4 + - - +
183A GLY* 3.7 0.9 - - - -
184A TYR* 3.1 39.3 + - + -
204A TRP* 3.6 40.8 - - + +
207A TYR* 4.2 11.0 - - + -
208A MET* 4.2 4.7 - - + -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU 2.9 16.1 + - - +
178A GLU* 3.8 5.2 - - - +
180A LEU* 1.3 76.2 - - - +
182A ASP* 1.3 65.1 + - - +
184A TYR* 3.3 2.4 + - - +
185A LYS* 3.0 39.9 + - - +
204A TRP* 3.7 35.4 - - + +
218A GLU* 5.2 0.9 - - - +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 3.0 38.2 + - - +
179A ASN* 3.9 11.2 + - - +
181A ALA* 1.3 76.7 - - - +
183A GLY* 1.3 57.6 - - - +
185A LYS* 3.4 17.0 + - - +
186A HIS* 2.8 30.9 + - - +
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.4 23.8 - - - -
152A TYR* 3.5 23.9 - - - -
169A PHE* 3.9 2.8 - - - -
179A ASN 2.9 12.0 + - - -
182A ASP* 1.3 73.7 - - - +
184A TYR* 1.3 60.9 + - - +
186A HIS* 3.8 1.0 - - - +
187A MET* 3.0 31.0 + - - +
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 4.0 7.9 - - + -
169A PHE* 2.6 42.0 + + + -
170A ASP 3.0 20.6 - - - -
171A GLY* 3.2 3.2 + - - -
180A LEU* 3.1 45.1 + - + +
181A ALA 3.3 2.4 + - - +
183A GLY* 1.3 74.8 - - - +
185A LYS* 1.3 63.0 + - - +
188A SER* 3.1 14.2 + - - -
200A TYR* 2.7 33.4 + - + +
202A CYS* 3.8 25.4 - - + -
203A SER* 3.3 1.7 + - - -
204A TRP* 3.2 60.5 + + + -
222A TYR* 4.8 0.8 - - - +
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA* 3.0 27.9 + - - +
182A ASP* 3.7 14.9 + - - +
184A TYR* 1.3 74.5 - - - +
186A HIS* 1.3 63.7 + - - +
188A SER* 3.4 3.3 + - - -
189A LEU* 3.1 31.2 + - + +
204A TRP* 3.9 13.5 - - + -
218A GLU* 2.7 33.9 + - - -
222A TYR* 3.7 49.0 + - + +
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Residues in contact with HIS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR* 3.5 38.6 - + + +
153A ASP* 3.3 30.5 + - - -
182A ASP 2.8 21.7 + - - +
183A GLY* 3.8 4.5 - - - +
185A LYS* 1.3 73.3 - - - +
187A MET* 1.3 56.8 + - - +
189A LEU* 3.3 10.8 + - + +
190A ALA* 2.8 24.8 + - + +
193A ARG* 4.4 6.3 + - - -
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Residues in contact with MET 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 4.3 1.8 - - - -
152A TYR* 3.5 43.7 - - + +
155A ASP* 4.2 15.0 - - + -
156A ALA* 3.9 15.3 - - - -
159A PHE* 5.2 0.9 - - + -
167A LEU* 3.9 22.2 - - + -
169A PHE* 3.5 37.7 - - + -
183A GLY 3.0 15.6 + - - +
186A HIS* 1.3 72.7 - - - +
188A SER* 1.3 59.7 + - - +
190A ALA* 4.0 2.5 - - - -
191A LEU* 2.8 42.2 + - + +
200A TYR* 3.4 17.7 - - + +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.9 11.8 - - - +
184A TYR 3.1 15.8 + - - -
185A LYS 3.4 9.2 - - - -
187A MET* 1.3 76.7 - - - +
189A LEU* 1.3 58.6 + - - +
191A LEU* 3.3 5.3 + - - +
192A ASN* 3.0 28.0 + - - +
200A TYR* 3.6 12.7 + - - -
222A TYR* 2.8 46.6 + - - -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 3.1 19.1 + - + +
186A HIS* 3.6 9.4 - - + +
188A SER* 1.3 80.4 - - - +
190A ALA* 1.3 57.4 + - - +
192A ASN* 3.2 11.2 + - + +
193A ARG* 2.9 51.3 + - - +
222A TYR* 4.7 19.5 - - + +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR 4.0 8.7 - - - +
153A ASP* 3.6 22.0 - - - +
156A ALA* 3.6 20.9 - - + +
157A GLN* 6.0 0.2 - - - +
186A HIS* 2.8 21.5 + - + +
187A MET* 3.6 7.9 - - - +
189A LEU* 1.3 70.4 - - - +
191A LEU* 1.3 64.7 + - - +
193A ARG* 3.4 20.9 + - - +
194A THR* 3.3 17.7 + - - +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ALA* 4.2 17.9 - - + +
159A PHE* 5.0 4.7 - - + -
167A LEU* 4.0 20.9 - - + -
187A MET* 2.8 28.4 + - + +
188A SER* 3.6 4.7 - - - +
190A ALA* 1.3 71.6 - - - +
192A ASN* 1.3 61.4 + - - +
194A THR* 2.6 29.2 + - - -
195A GLY 4.0 0.3 + - - -
196A ARG 4.1 7.2 - - - +
198A ILE* 3.6 40.6 - - + +
200A TYR* 3.4 45.5 - - + -
1C NAG 5.5 0.2 - - - -
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Residues in contact with ASN 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 6.0 4.6 - - - +
34A ASN* 5.5 1.0 - - - +
188A SER 3.0 13.4 + - - +
189A LEU* 3.2 17.2 + - + +
191A LEU* 1.3 76.9 - - - +
193A ARG* 1.3 60.8 + - + +
195A GLY* 3.0 22.0 + - - -
1C NAG 1.4 73.5 + - - +
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Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASP* 2.9 30.3 + - - -
186A HIS* 4.4 9.1 + - - -
189A LEU* 2.9 38.8 + - - +
190A ALA* 3.7 16.4 - - - +
191A LEU 3.3 0.8 - - - -
192A ASN* 1.3 76.7 - - - +
194A THR* 1.3 63.0 + - - +
195A GLY* 3.2 0.9 + - - -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ALA* 3.6 30.1 - - + +
157A GLN* 4.1 11.4 - - + +
160A ALA* 3.5 20.1 - - + +
190A ALA 3.3 16.2 - - - +
191A LEU* 2.6 19.8 + - - +
192A ASN 3.1 0.2 - - - -
193A ARG* 1.3 78.0 - - - +
195A GLY* 1.3 59.0 + - - +
196A ARG* 3.1 21.4 + - - +
198A ILE* 4.3 3.4 - - + +
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASN 3.0 15.9 + - - -
193A ARG 3.2 1.9 - - - -
194A THR* 1.3 75.8 + - - +
196A ARG* 1.3 60.4 + - - +
197A SER* 3.9 1.6 + - - -
1C NAG 3.5 13.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il